Objective To analyze the clinical values of magnetic resonance imaging (MRI) and multi-slice spiral CT (MSCT) in the diagnosis of pancreatic cystic disease. Methods 24 cases of patients with pancreatic cystic lesions admitted to our hospital from October 2013 to October 2017 were retrospectively analyzed. All patients were given the MSCT and MRI before operation, and the examination results were compared with the surgical pathology examination, and the imaging findings of MSCT and MRI were analyzed. Results Pathological diagnosis showed that there were 9 cases of pancreatic pseudocyst (PPC), 2 cases of true pancreatic cyst (TPC), 3 cases of serous cystic neoplasms (SCN), 5 cases of mucinous cystic neoplasms (MCN), 4 cases of intraductal papillary mucinous neoplasm (IPMN) and 3 cases of solid pseudopapillary neoplasm (SPN) in 24 cases of patients with pancreatic cystic lesions. There was no significant difference in the accuracy of MSCT and MRI (P>0.05). The MRI examination time was significantly longer than MSCT examination (P<0.05). Conclusion Both MRI and MSCT can accurately diagnose the pancreatic cystic lesions. Although MRI examination time is longer, it can provide clinicians with more pathological information. In the actual clinical application, it should be combined with the actual situation of patients to choose reasonably the best way so as to provide imaging basis for follow-up treatment.